McIlroy bid for a career Grand Slam ended when he shot a disappointing second-round 77 after being a favorite to win his first Green Jacket at Augusta National heading into the major.
He will not be replaced by an alternate, with the field reduced to 143 players for the tournament on Hilton Head Island, where Jordan Spieth (29) is the defending champion.
McIlroy, who captured the last of his four majors in 2014, had been hoping to win the Masters so that he could join Gene Sarazen, Ben Hogan, Jack Nicklaus (83), Gary Player (87) and Tiger Woods (47) as the only players to achieve the career Grand Slam.